When you're heading for Alona Beach on Panglao you will pass through Tacbilaran. The normal way would be with the Supercat ferry (http://www.supercat.com.ph/) from Cebu City or Dumaguete. Once off the ferry you can get a taxi or a tricycle (3 wheel motorcycle with side car). If you're travelling alone the tricycle is the cheapest solution (something like 150-200 PHP) but if you're travelling in a group a taxi will be pretty much the same.
In either case you should expect to spend around 40 minutes passing through a beautyful countryside before arriving in Alona Beach. Notice that there might still be 200 m to go (e.g. to Alonaville) when they wont take you any longer! Ask them to carry your bag if you're bringing your own dive equipment.
I just talked up a jeepney driver in Tagbilaran and he agreed to drive me around Bohol for 2.500 PHP/12hrs. plus gasoline...
If you decide to go on island hopping, dolphin watchin or snorkelling, boat owners are everywhere the beach of Alona offering their services. Price of rental of 1 boat is P1500.
preferably for those humble travelers who don't mind squishing themselves in crammed mini-bus along with the locals. they park somewhere near shopper's across bohol museum in tagb. city
we hired a tricycle from tagbilaran city to take us to panglao....we paid 150 to take us there which includes the trip to the hinagdanan cave.....